Deeper still into the Mothership... you are now in the core of the great vessel, and there's no turning back. But the Skaarj are getting worse - there's no doubt about that. Time to ready your most powerful weapons and take the proverbial plunge...

You start in the corridor by which you left the MotherShip Lab. The passage you are in goes up steps to the right, so follow them round, arriving at a lift shaft. A lift comes down, with an unarmed SkaarjTrooper aboard.

The Skaarj is weak and easily disposed of with a single Flak Shell, so kill it then let the lift go back up. Go on to the floor beneath where the lift was to grab a Shield Belt. Go back on to the steps, and the lift comes back - get aboard and ride it to the top, then step off into a low corridor.
This corridor is part of what I'll call the Loop. It's a ring of corridors and rooms that goes around a central core room, and you're going to go round it several times as this level progresses.
Take a right in the Loop corridor here, and go through doors at the end into a dark-ish room where you will be attacked by a SkaarjLord - kill the Skaarj then enter the room it was guarding. This room is empty except for a Health Pack at the back left, but there's an exit in the front left corner, so go through it and go down the slope of the corridor beyond. You will find that your corridor makes a right through a hatch that opens as you approach it, near an alcove containing various goodies where a SkaarjBerserker operates a control panel. Unfortunately, the alcove is blocked by a forcefield, and I can tell you now that you won't be getting in there in this level.
So, instead, follow the corridor to the right through the hatch that opened. It takes you out on a balcony overlooking the central core room, where you will have an altercation with a SkaarjTrooper with an Eightball Gun. Kill him and collect the Eightball Gun that he drops. If he jumps off the balcony into the core room itself then don't worry, you can deal with him later.

Go to the end of this balcony and collect the Health Pack at the far end. A walkway turns off to the left here, continuing to follow the outside of the core room. After a bit of winding, it takes you out in a corridor where you will probably meet a SkaarjTrooper with a Razorjack. Kill him then collect the Razorjack that he drops.

Note: Throughout this part of the walkthrough you will find that Skaarj like to move about and run off when they see you, bringing others back or leaving you confused. I cannot cover it all so you'll have to take some initiative on this one; be prepared for a surprise, then do what you think best.

Look to the right from the walkway you entered this corridor by. There's a locked door there, with a brightly glowing readout over it.

"ACCESS DENIED: The Intruder must be eliminated. All WarMasters are being routed to this area upon arrival from the Source."

Exercise caution in the next stretch because there's another SkaarjTrooper with a Razorjack on patrol here somewhere. When you meet him, you should kill him and take his Razorjack. Anyway, from the locked door continue your anticlockwise journey round the Loop by going the other way up the corridor and following its curve. Shortly you will meet a SkaarjTrooper / SkaarjGunner hybrid carrying a Flak Cannon, and maybe a SkaarjWarrior. Kill both Skaarj then collect the Flak Cannon the SkaarjTrooper / SkaarjGunner hybrid drops, then enter the area the Skaarj were guarding. This is a brief detour from your journey round the Loop, but bear with me.
This area is a set of ramps that go down in two stages and then under the Loop to come out in the core room. There's little of interest in the core room itself, but explore this ramp area for goodies.

Take the ramp on the left and you will find a Health Pack at the top. Continue down, and when you can, climb a diagonal support on to a raised platform where you can pick up an Assault Vest and another Health Pack. Drop down from there on to the flat half-way stage where the ramp system doubles back on itself. If you go through a small wall-opening there you will find a box of Razor Blades and an alcove containing assorted gear, but the alcove is blocked off by a nasty electric field.
Go back out and down the lower ramp a little, turning back and climbing back up the diagonal support strut to the right when you get the opportunity. Hop over the hand rail and go into an alcove beneath the upper ramp on this side for a Health Pack, a Flare, an ASMD Core and a box of 10 Flak Shells. Then, go back out and across the ramp, clinbing over into another similar alcove beneath the ramp opposite for another Health Pack, a Flak Shell and a box of 8 Rifle Rounds. When you're done, return to the ramp.
Climb back up the ramps and re-join the Loop. Follow the Loop corridor to the right, resuming your anticlockwise journey. After the corridor has curved round a while, you can duck behind a panel for a box of Razor Blades. Follow the corridor as it turns into another raised walkway over the core room, then go round it unto another corridor away from the core with doors at the far end, where alcoves along the side contain a can of 12 Eightballs, 40 Tarydium Shards and a box of 50 Bullets. Go along and through the doors at the far end to enter yet another room filled with large techno structures.

This room is guarded by a SkaarjTrooper with a Dispersion Pistol and a SkaarjOfficer with a GES Biorifle. Kill the two then collect the GES Biorifle dropped by the SkaarjOfficer. Go round the edge of this room to collect two cans of Tarydium Sludge and a box of 50 Bullets. Go through the doors out of this room that were to the left as you entered. One corner and one Health Pack later, and you are back at the top of the small lift you used right at the start of the level. You've completed a circuit of the Loop.
You're going to have to do some freelancing now. Remember that locked door with the glowing message over it? Well, you have to go through there. But it'll only open when you have killed all the Skaarj that this part of the level throws at you. You have to complete several circuits of the Loop; you will find consistent numbers of reinforcements in the form of SkaarjInfantry with Stingers and the occasional SkaarjAssassin or SkaarjLord. Kill them all, none must escape. Collect any Stingers dropped by the SkaarjInfantry.
With each circuit of the loop that you complete, check the locked door. When you have killed enough Skaarj (if you are going round the loop and meeting no Skaarj but the door still hasn't changed then check the core room for any skulkers), you will see that the readout has vanished and the door is in darkness. Shortly after that, it bursts open, revealing a SkaarjOfficer with a Stinger and a SkaarjGunner with a Razorjack. Kill them.
When they are both dead and you have collected the Stinger and Razorjack that they drop, go through the now open doors yurself and down the sloping corridor beyond. At the bottom, you will reach a walkway over some fields where you will fight and kill a SkaarjWarrior.

Go along the walkway, collecting a Health Pack along the way. Then, a curving corridor at the far end will lead you via another Health Pack to another of those energy lifts. Step on it and ride to the top. Step out at the top, and you are in a kind of science area where you can go several ways; a SkaarjLord dozes on the right, so kill him. Go to the right and into a small passage there for a Health Pack and 40 Tarydium Shards, but come straight back one you've collected the gear.
Returning from the small passage, drop off to the left into a recessed area where there are cryopods by the walls. Collect of the Health Pack, box of 50 Bullets and box of 10 Flak Shells there then activate and read the panel nearby.

When you're done here, go and press the button on the other side of the recess to call a lift to take you back up to the main hallway above. Ride that lift and turn left, going back past the top of the energy lift shaft and going along to the door at the far end, which is blocked with a large readout over it.

Follow this area on round, forking to the left as you return from the locked door. A forcefield on the left (by which there is a can of 12 Eightballs) blocks the way back to an area you will recognise from MotherShip Lab. Continue along and in the room beyond watch out for a SkaarjInfantry with a Stinger, then go into the room's corners for 40 Tarydium Shards, a Health Pack and an ASMD Core. You can see a Super Health Pack in a raised passage but you can't reach it from here yet.
A narrow passage (containing a Health Pack) from the far corner of this area leads round to a raised crossroads of walkways above a part of the Loop. Looking over to the right from this position you will see the other mouth of the raised passage containing the Super Health Pack - but you still can't get it.
Return to this crossroads from the passage by the same access route, then look at the other exits. The rightermost one leads back to the cryopods, so go instead to the one directly ahead. It is locked with a readout.

"Securit Post, ACCESS DENIED"

Look at the other exit. It too is locked with a message.

"Primary Power Supply, ACCESS DENIED"

You're not completely stumped though, as 45° anticlockwise from here a forcefield bridge leads away from the crossroads.

Cross the bridge into the area beyond. Alcoves on either side reveal a Health Pack and a box of Razor Blades. Collect, then activate and read the panel at the back.

"Access to the Security Post granted."

Shoot the rear panel of the alcove where the Health Pack was. It will lift up to reveal Jump Boots. Collect them, then return across the force field bridge to the crossroads. You can now get the Super Health Pack - but approach the Super Health Pack passage from the other end - you won't be able to jump to it from here.
Return the crossroads and go to the entrance on the other side to the left, which is now open. Go through into the passage and approach a tempting Super Health Pack, but a door slams shut over it whilst another opens to the right to reveal an angry SkaarjWarrior. Kill it, then enter the room from which it emerged. This room contains a lift to a raised walkway, but first visit alcoves in the room for two Flak Shells, a box of 8 Rifle Rounds and two cans of Tarydium Sludge.
Take the lift and make a left as you step off at the top on to the raised walkway, entering another small passage which curves round, leading to a Health Pack and a button. Press the button. What it does is to re-open the hatch over the Super Health Pack - but before going back down, go on to the raised walkway and enter the passage at the other end. After a short curve with a Health Pack, you will be in a room where purple laser beams oscillate across your view.

This bit's not too tough, but save your game anyway. Then, go into the room and negotiate the lasers - try not to get squished (I use the alcoves at the side and do it step by step). Your reward at the far end is a Health Pack, a Shield Belt and a box of 10 Flak Shells. Return through the beams, and drop to floor level beneath the raised walkway.
Go out into the passage and turn right, collecting the Super Health Pack. You are on a high ledge above the core room from earlier. As you approach, a platform extends across the gap to a ledge on the other side - go across and enter the small dark passage on the left, but beware the SkaarjWarrior who attacks from the darkness.
Use a light source to negotiate the corridor and follow its curve on round. You will arrive in the Security Post - a room full of panels guarded by a SkaarjAssassin in plain view and a SkaarjInfantry with a Stinger round the corner. kill both Skaarj and collect the SkaarjInfantry's Stinger. In doing so you will see a button in the area in which the SkaarjInfantry was lurking, but don't press it yet - read the three panels in this area first.

"WARNING: Armed Intruder detected. Close all access to the Source and to the Primary Power Supply. Preventing the intruders from accessing the Core Generator is critical."

"SECURITY ALERT: All WarMasters report to Core Generator positions to insure its protection."

Now it is time to press the button. So, do so. An alert siren goes off and the panels change.

"Core Access Door Open"

"RED ALERT: Core Generator Security Compromised"

"Intruder detected near the Core Generator. Core Generator security must be maintained. Weakness shall be punished."

Small passages at either end of the security post (you came in by one) lead you back out to the high ledges above the core room. Take your pick. Then, go back out to the raised crossroads and go round to the now open Primary Power Supply entrance (next one anticlockwise). Look in through the entrance and kill the Brute on guard in the large corridor beyond.
Enter the corridor and go along. The corridor is lined with gear as you proceed; a box of 8 Rifle Rounds, two boxes of 10 Flak Shells, two clusters of 40 Tarydium Shards, a Flare, two boxes of Razor Blades, two cans of 12 Eightballs, two cans of Tarydium Sludge, two ASMD Cores and a Health Pack. Beyond this gear, the corridor curves round and goes on inwards.

Follow the corridor on through the Mothership. Soon you will reach a junction with a cache of gear behind a forcefield on the left, where a SkaarjWarrior attacks from a continuation of the corridor to the right. Kill the Skaarj - you're not going to get that forcefield open in a hurry, so go the other way. After a curve, you will reach a pair of doors. Go through them to exit the level.